Wednesday, January 21, 2015

Mathematical modeling is a useful tool, but only if the input data is solid. And even though M&E have listed a hundred references, as we pointed out, many are previously modeled assumptions based on or around papers by the ISG or their followers, involved in the RBCT Badger Dispersal Trial or, in the case of other stuff, so historic as to be meaningless after almost 20 years of inertia on badger control.

So let's look at some of the input data, entered by M&E:
Their model area is approx 67 miles square (or 11,500 km2) and contains 1.4 million (dairy) cattle.
That's an area slightly more than the size of Devon plus Somerset.
The total cattle population of GB at the end of 2013 was 9.7m, of which the dairy herd was said to be 1.8m and the beef herd 1.6m; the rest are calves, young stock and fattening cattle. So they've got almost the entire national dairy herd squashed into two counties, and they're not allowing for sheep, arable, woodland etc, never mind the occasional town or village?

They've also assumed 5.7 adult badgers per km2, which seems on the low side for what appears to be a lovely area of wall-to-wall dairy farms and much lower than FERA have published for Gloucestershire where they trapped 844 in 55 sq km during their vaccination 'Elf n' Safety' trial in 2007/8. That is over
15 per sq km. (or 15.5 if one counts half a badger). And in parts of
Oxfordshire, population densities of 38 per sq km have been recorded.

Following those badger numbers, the M&E model starts out with badgers in only 3113 out of 16384 of their "cells" - which seems unlikely.

Cattle-to-cattle infection: M&E say that cattle can transmit TB at even early stages of the disease and so their model reflects this belief. But actual hands on research on reactor cattle [SE3013] -[link] referred to by the ISG - but not in detail for obvious reasons, found that of 1543 nasal samples taken, and a further 1000 in a parallel study
[SE3033] not a single one was capable of onward transmission.

To avoid confusion, we'll quote again the conclusion of this £2.8m study:

"M.bovis was not detected by bacterial culture in any of the nasal mucus samples." and "The results suggest that large concentrations of M.bovis are not present in the nasal passages, and the shedding of M.bovis, if it occurs, is rare in naturally infected GB cattle."

This is also born out by pairings of reactor cattle with in contacts, done in Ireland - [link]Ireland by Eamon Costello and Dr. O'Reilly.

Thus M&E's 'Winter housing' assumption is just that, and not the experience of studies which housed reactors together for months, slaughtered, salami sliced and collected samples to prove or disprove their work.

Their model also seems to assume that all cattle on a farm are housed together in one place. This is not what happens in practice, as is their assumption of cattle moving round their entire farm 'cells' randomly all of the time. Again, not what happens in practice, particularly on a dairy farm.

But the 'assumption' we appreciate most, is that of badger-to-cattle transmission: M&E do not seem to have a clear idea what the rate of badger-to-cattle transmission is, even claiming that it is a "little studied variable". Whaaaaat???

This has been 'studied' to death - in fact the death of up to 40,000 cattle a year, even if it did not need to be, and as we pointed out in this posting, where we listed the 'postulates' of disease transmission - [link] , a table used by epidemiologists and veterinary scientists - if not modelers.

All papers written over the past four decades - Zuckerman, Dunnett, Krebbs etc - have concluded that infected badgers pose a significant risk to cattle. And even dear old Defra, in a booklet issued in 2001, instructing readers about reducing the TB risk [to cattle] state:

"The consensus of scientific opinion is that badgers are a significant source of TB infection in cattle...."

So as the conclusions of the model M&E have used, seems to turn all this on its head, one has to question the input data they have used. On the other hand, in a few short months, an election is looming...

But we digress: on badger culls, their model seems to assume that if just one badger is shot in a cull, then all the other badgers in its group will move out? That is taking the perturbation myth a tad too far we think. Particularly as at least twice annually, the badger groups have a shake out of the old, the sick and the young males. And they seem to 'leave' without causing a problem or even a space?

A paper by 'Gilbert' is quoted many times as a source of the M&E assumptions on cattle movements as 'a significant source of TB spread'. This paper is modeled on post FMD restocks, when a handful of cattle were found to have moved, carrying TB. The point here is that their post move skin test identified them, they were slaughtered and that was that. They did not pass their TB on to other cattle on new farm. A point lost on M&E, as is the compulsory pre movement testing of all cattle moving around or from annual testing areas. A policy in place since 2006.

Thus based not on any of the epidemiological work which Defra has produced, taxpayers have funded we have quoted, but assumptions modeled on previous assumptions, M&E published that the "three main factors influencing TB were the percentage of cattle movements, the frequency of testing, and the badger-to-cattle transmission rate."

But hidden within the paper they also say that:

"Culling of badgers does seem to be a strategy that will eventually lead to a lower incidence of TB in cattle."

Really?????

MAFF / DEFRA knew this thirty years ago, when the Thornbury area of Gloucestershire was cleared so successfully, leading to over a decade of TB free cattle. We asked why:

" The fundamental difference between the Thornbury area and other areas [] where bovine tuberculosis was a problem, was the systematic removal of badgers from the Thornbury area. No other species was similarly removed. No other contemporaneous change was identified that could have accounted for the reduction in TB incidence within the area" [157949]

So from a professional modeler, a comment on computer modeling generally:

" There are usually a few key variables and you can adjust them to give you almost any answer you want."

And finally a reminder that less than a year ago, the Guardian - [link] ran a story on computer generated guff, which was published and regurgitated, because no-one was prepared to challenge it or admit they couldn't understand a bloody word of it.

If the input data is 'unsafe' then its modeled conclusions, however seductive to the politics of the day, are even more so.

Saturday, January 17, 2015

The headlines this week have included an astonishing abstract from Mistakers Moustakas and Evans of Queen Marys University of London (QMUL) in which their computer model suggests that more frequent TB testing and
keeping cattle outside in the winter are the best ways to control bovine TB (bTB) And that culling badgers has minimal effect.

But the paper itself is a wonderful fairy land of cells in which badgers move, cells, (square or round) in which cattle move and apparently, so does zTuberculosis. At least in theory. If the cells are correct, the movements are correct and the input data used was solid, this may have been a useful exercise, but...
The paper asserts:

Computational models provide a valid alternative to expensive experimental approaches (Godfray et al.
2004) as a method of testing the likely effects of various strategies designed to control or eradicate TB in cattle. To be useful such models need to represent the modelled system in sufficient detail to allow realistic predictions to be made about the outcome of any control strategy (Evans et al. 2013b

True. but if the data input is incorrect, aged or derived from flawed assumptions? What then?

This justification is part of the basis of this particular 'theory' now expounded by Mistakers Moustakas and Evans who explain:

However, entering other people's 'assumptions', even if they've been published, is never a good way to begin, especially if actual available data tells you it is way out of date, or just plain wrong.

Much of the modeling seems to stem from 'Meyer et al : 2007 - who is mentioned quite a lot. As we haven't heard of an epidemiologist called Meyer, we assume that he may have developed mathematical models, the calculations for some of which is explained below:

Sensitivity analysis of model input parameters (Latin hypercube sampling) indicated that observed and simulated values in terms of percentage of infected cattle were not significantly different from each other (t test statistic = -1.26, P = 0.45).ANOVA results of the most parsimonious mixed model with the number of infected cattle as a dependent variable, show that there were significant effects of the percentage of cattle that are moved in a year (F4, 156 = 54.62, P\0.0001), the distance which cattle were moved (F4, 156 = 7.74, P = 0.006), both the cattle-to badger and badger-to-cattle infection rates (F3, 156 = 4.46, P = 0.036; F3, 156 = 8.59, P\0.004), the inter-test
interval (F4, 156 = 59.80, P\0.0001) and the accuracy of the test (F3, 156 = 3.81, P = 0.053), badger culling
(F2, 156 = 8.91, P = 0.003) and the initial number of infected badgers (F2, 156 = 16.08, P = 0.0001).

Still with us?

We note that present, factually incorrect and expanded are the 'assumptions' made by the diminutive professor, John Bourne who explained so helpfully in his Final Report (2007) [ 7:24] that actually looking at herd breakdown risk assessments was just too time consuming, so his team had assumed two parts cattle (contiguous or purchased) and one part badger ......... and switched on their model.

This is a chart of what they assumed and 'roughly estimated'.

The data from the same period for the county of Devon, which they received but failed to examine, showed a
completely different picture, with at least 76 percent and up to 90 per cent of herd breakdowns due to infected badgers. This according to the data sheets, painstakingly filled in by AH staff.

This paper of Mistakers Moustakas & Evans is peppered with mathematical terminology designed to baffle brains. They speak of 'regressions, co-efficients and remaining parameters' but also, echoing the ISG models, use words such as 'assumptions and estimates', building on previously well churned ISG sand.
The sources of cattle and badger data are also predominantly post 2007, and thus ISG / Woodroffe material.

We suppose we should be grateful they didn't include the modeled scenario published in July 2014 by Dr. Ellen Prook-Bollocks, Brooks-Pollock, who put 100 per cent of cattle into her model, switched on, and then exclaimed that if we culled all the cattle, - [link] zTB would vanish.

This well publicised model took cattle to cattle transmission, cattle into the environment and cattle movement, describing them as 'idealised control measures'.

But we digress: in the Evans paper, badger numbers seem way too low, as is tuberculous infection within the badger population, now given by FERA at around 50 percent in areas of endemic infection.(Chambers et al)

And much as we hate to break into the QMUL modelers' bubble, actual data on what makes a difference does exist, and has done for some time. As is shown above and in PQs below.

A decade ago, Shadow minister Owen Paterson, MP asked for the results of the Thornbury badger clearance and why it had been so successful at reducing TB in cattle to zero: a situation which lasted at least a decade. They didn't ask a computer, but the answer was unequivocal:

"No confirmed cases of tuberculosis in cattle in the area were disclosed by the tuberculin test the the ten year period following the cessation of gassing" [150573]

So not 20 years of buggering about trying to cull out infected badgers in ones and twos, very occasionally? (Or even taking pot shots at the scent markers ?)

" The fundamental difference between the Thornbury area and other areas [] where bovine tuberculosis was a problem, was the systematic removal of badgers from the Thornbury area. No other species was similarly removed. No other contemporaneous change was identified that could have accounted for the reduction in TB incidence within the area" [157949]

And bringing this right up to date are the published results from the Somerset cull, lasting merely a well publicised (and interrupted) few weeks in 2013, when 34 per cent of herds in the cull area were under TB restriction.

A herd data check before the second cull in 2014 and reported here - [link] showed that this figure had reduced to just 11 percent - a drop of almost 68 percent.

We are pleased that Mistakers Moustakas and Evans appear to appreciate the accuracy of the skin test though, observing that:
"

Accuracy of the test to detect infected cattle explained less than 3 per cent of the variance in the number of infected cattle."

But we also note that their model predicts MORE cattle infected while tucked up in their winter housing.
However, the current advice and biosecurity guidelines issued by the APHIDs APHA, and expanded by Professor Godfray recently, is to place all dairy cattle - [link] in hermetically sealed boxes, into which badgers cannot gain access.

Thus cattle farmers receive diametrically opposed views even on that one small piece of husbandry advice.

So as all this taxpayer funded 'research' spills into the press with headline grabbing sound bites which inevitably exclude badgers, hang on to those basic facts. Everything else is smoke and mirrors. And sometimes, simple squared really does equal stupid.